We carried out DNA microarray-based global expression profiling of all preimplantation stages in mouse. It revealed and characterized the distinctive patterns of maternal RNA degradation and two major transient waves of de novo transcription: zygotic genome activation (ZGA) and mid-preimplantation gene activation (MGA). We also developed a technique to do large-scale Whole Mount In Situ Hybridization (WISH), which allows us to reveal the spatial expression patterns of 91 genes in mouse preimplantation embryos. Through these analyses, we identified a number of genes that show unique expression patterns. We have demonstrated that one of them, named Zscan4, is expressed exclusively in 2-cell mouse embryos and ES cells and plays a critical role in the progression of preimplantation development. Another gene (Chuk) shows constant RNA levels throughout preimplantation development and can be used as an internal standard suitable for quantitative RT-PCR. We also identified genes, named Trim43a, Trim43b, and Trim43c, whose expression began at the 2-cell stage, peaked at the 8-cell/morula stage, and dramatically fell by the blastocyst stage. We identified a 5 kb DNA fragment that covers upstream region of Trim43a as a putative promoter, which can drive the expression of mStrawberry fluorescent protein in a manner similar to endogenous Trim43 genes. Trim43 genes will be useful stage-specific markers for the study of preimplantation embryos. We are currently studying the functions of these genes in detail.